Starting phenix.real_space_refine on Mon Jan 13 18:02:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8l_18254/01_2025/8q8l_18254.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2139 2.51 5 N 624 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3405 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.52, per 1000 atoms: 1.03 Number of scatterers: 3405 At special positions: 0 Unit cell: (112.064, 116.184, 42.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 624 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 424.7 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.611A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.688A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 320 removed outlier: 6.586A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.505A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.490A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.155A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.210A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.482A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 373 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 307 through 310 Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.004A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.404A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.374A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.551A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.403A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.751A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.515A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.417A pdb=" N ASN B 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE D 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 377 removed outlier: 6.697A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 965 1.33 - 1.45: 417 1.45 - 1.57: 2071 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3459 Sorted by residual: bond pdb=" CA GLY E 366 " pdb=" C GLY E 366 " ideal model delta sigma weight residual 1.510 1.563 -0.053 1.39e-02 5.18e+03 1.46e+01 bond pdb=" CA LYS B 331 " pdb=" C LYS B 331 " ideal model delta sigma weight residual 1.532 1.554 -0.022 6.50e-03 2.37e+04 1.17e+01 bond pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.40e+00 ... (remaining 3454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 4149 3.29 - 6.59: 459 6.59 - 9.88: 17 9.88 - 13.18: 3 13.18 - 16.47: 1 Bond angle restraints: 4629 Sorted by residual: angle pdb=" N CYS E 322 " pdb=" CA CYS E 322 " pdb=" C CYS E 322 " ideal model delta sigma weight residual 108.32 124.79 -16.47 1.64e+00 3.72e-01 1.01e+02 angle pdb=" C GLY E 323 " pdb=" N SER E 324 " pdb=" CA SER E 324 " ideal model delta sigma weight residual 122.44 134.40 -11.96 1.45e+00 4.76e-01 6.80e+01 angle pdb=" C GLY E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta sigma weight residual 120.64 130.18 -9.54 1.26e+00 6.30e-01 5.73e+01 angle pdb=" N GLY E 323 " pdb=" CA GLY E 323 " pdb=" C GLY E 323 " ideal model delta sigma weight residual 112.22 125.05 -12.83 1.74e+00 3.30e-01 5.44e+01 angle pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta sigma weight residual 121.24 111.22 10.02 1.44e+00 4.82e-01 4.84e+01 ... (remaining 4624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.44: 1778 11.44 - 22.88: 253 22.88 - 34.31: 53 34.31 - 45.75: 11 45.75 - 57.19: 8 Dihedral angle restraints: 2103 sinusoidal: 876 harmonic: 1227 Sorted by residual: dihedral pdb=" C LYS E 347 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual -122.60 -143.32 20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CA CYS E 322 " pdb=" C CYS E 322 " pdb=" N GLY E 323 " pdb=" CA GLY E 323 " ideal model delta harmonic sigma weight residual 180.00 149.93 30.07 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 2100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 466 0.173 - 0.346: 52 0.346 - 0.519: 3 0.519 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.160 2.00e-02 2.50e+03 8.90e-02 1.58e+02 pdb=" CG TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.144 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " -0.081 2.00e-02 2.50e+03 6.04e-02 5.46e+01 pdb=" CG HIS E 362 " 0.096 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " -0.039 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1722 3.01 - 3.48: 2786 3.48 - 3.96: 5333 3.96 - 4.43: 5408 4.43 - 4.90: 10265 Nonbonded interactions: 25514 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.539 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.554 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.563 3.040 ... (remaining 25509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = chain 'B' selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = (chain 'E' and resid 306 through 378) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.010 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.053 3459 Z= 0.769 Angle : 2.075 16.473 4629 Z= 1.364 Chirality : 0.115 0.866 522 Planarity : 0.012 0.089 588 Dihedral : 11.489 57.185 1323 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.040 0.004 HIS E 330 PHE 0.045 0.014 PHE E 378 TYR 0.160 0.039 TYR A 310 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.409 Fit side-chains REVERT: C 321 LYS cc_start: 0.7785 (mttt) cc_final: 0.7209 (ttmm) REVERT: C 349 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7041 (mtp-110) REVERT: C 358 ASP cc_start: 0.7265 (m-30) cc_final: 0.6335 (m-30) REVERT: E 311 LYS cc_start: 0.8214 (pttt) cc_final: 0.7736 (ptmm) REVERT: E 317 LYS cc_start: 0.7356 (pttt) cc_final: 0.6673 (ptmt) REVERT: B 375 LYS cc_start: 0.7998 (tttt) cc_final: 0.7628 (tttp) REVERT: D 322 CYS cc_start: 0.8257 (p) cc_final: 0.7470 (m) REVERT: D 347 LYS cc_start: 0.7106 (ptmt) cc_final: 0.6475 (tppt) REVERT: D 372 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 375 LYS cc_start: 0.8564 (tttt) cc_final: 0.8105 (ttmt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3134 time to fit residues: 21.4823 Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 330 HIS E 362 HIS B 327 ASN B 362 HIS D 330 HIS D 362 HIS F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.128886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.112521 restraints weight = 4677.195| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.58 r_work: 0.4166 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3459 Z= 0.218 Angle : 0.806 9.280 4629 Z= 0.421 Chirality : 0.056 0.208 522 Planarity : 0.004 0.043 588 Dihedral : 8.023 41.904 456 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.26 % Allowed : 10.00 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 362 PHE 0.009 0.002 PHE E 378 TYR 0.017 0.004 TYR E 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.411 Fit side-chains REVERT: C 321 LYS cc_start: 0.8110 (mttt) cc_final: 0.7675 (ttmm) REVERT: C 349 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7178 (mtp-110) REVERT: E 311 LYS cc_start: 0.8368 (pttt) cc_final: 0.7984 (ptmm) REVERT: E 317 LYS cc_start: 0.7586 (pttt) cc_final: 0.7255 (ptmt) REVERT: E 360 ILE cc_start: 0.8417 (tt) cc_final: 0.8006 (mp) REVERT: B 322 CYS cc_start: 0.8430 (p) cc_final: 0.7849 (m) REVERT: D 317 LYS cc_start: 0.7667 (pttt) cc_final: 0.6976 (ptpp) REVERT: D 322 CYS cc_start: 0.8569 (p) cc_final: 0.7954 (m) REVERT: D 347 LYS cc_start: 0.7115 (ptmt) cc_final: 0.6467 (tptt) REVERT: D 375 LYS cc_start: 0.8416 (tttt) cc_final: 0.7998 (ttmt) REVERT: F 375 LYS cc_start: 0.8867 (tttt) cc_final: 0.8464 (ttmt) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.3685 time to fit residues: 19.2972 Evaluate side-chains 43 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.253198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.215691 restraints weight = 3855.674| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 0.97 r_work: 0.4912 rms_B_bonded: 0.47 restraints_weight: 0.5000 r_work: 0.4878 rms_B_bonded: 0.86 restraints_weight: 0.2500 r_work: 0.4694 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3459 Z= 0.364 Angle : 0.805 11.186 4629 Z= 0.415 Chirality : 0.058 0.199 522 Planarity : 0.005 0.041 588 Dihedral : 7.262 29.719 456 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 12.31 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 362 PHE 0.011 0.002 PHE E 346 TYR 0.027 0.005 TYR C 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.424 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.3216 time to fit residues: 19.0971 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.255146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.217572 restraints weight = 3894.463| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 0.99 r_work: 0.4913 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.4875 rms_B_bonded: 0.88 restraints_weight: 0.2500 r_work: 0.4689 rms_B_bonded: 3.10 restraints_weight: 0.1250 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3459 Z= 0.293 Angle : 0.725 9.091 4629 Z= 0.368 Chirality : 0.054 0.148 522 Planarity : 0.004 0.042 588 Dihedral : 6.849 30.294 456 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.99 % Favored : 96.78 % Rotamer: Outliers : 2.82 % Allowed : 11.28 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.005 0.001 PHE E 346 TYR 0.020 0.004 TYR E 310 ARG 0.004 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.369 Fit side-chains REVERT: E 360 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7770 (mp) REVERT: D 317 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7614 (ptmt) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.3728 time to fit residues: 18.6743 Evaluate side-chains 35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.256500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.219760 restraints weight = 3909.393| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 1.01 r_work: 0.4922 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.4882 rms_B_bonded: 0.88 restraints_weight: 0.2500 r_work: 0.4694 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3459 Z= 0.207 Angle : 0.655 8.158 4629 Z= 0.332 Chirality : 0.051 0.132 522 Planarity : 0.004 0.044 588 Dihedral : 6.360 27.871 456 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 13.59 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.005 0.001 PHE A 346 TYR 0.015 0.003 TYR C 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.413 Fit side-chains REVERT: E 360 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7751 (mp) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.3740 time to fit residues: 13.5729 Evaluate side-chains 32 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.0070 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.259946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.223312 restraints weight = 3907.901| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 1.14 r_work: 0.4944 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.4907 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.4691 rms_B_bonded: 3.86 restraints_weight: 0.1250 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3459 Z= 0.155 Angle : 0.600 6.665 4629 Z= 0.304 Chirality : 0.050 0.126 522 Planarity : 0.004 0.043 588 Dihedral : 5.851 30.390 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 330 PHE 0.005 0.001 PHE B 346 TYR 0.015 0.003 TYR B 310 ARG 0.005 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.408 Fit side-chains REVERT: E 360 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7750 (mp) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 0.3158 time to fit residues: 12.6250 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5036 > 50: distance: 1 - 86: 3.093 distance: 13 - 97: 3.215 distance: 96 - 100: 12.205 distance: 100 - 101: 12.066 distance: 101 - 102: 14.179 distance: 101 - 104: 24.386 distance: 102 - 103: 19.189 distance: 102 - 108: 33.057 distance: 104 - 105: 12.590 distance: 105 - 107: 7.591 distance: 108 - 109: 27.926 distance: 109 - 110: 24.093 distance: 110 - 111: 34.365 distance: 110 - 112: 7.748 distance: 112 - 113: 6.127 distance: 113 - 114: 8.940 distance: 113 - 116: 6.277 distance: 114 - 115: 7.970 distance: 114 - 120: 10.178 distance: 116 - 117: 14.993 distance: 117 - 118: 7.272 distance: 117 - 119: 4.256 distance: 120 - 121: 7.666 distance: 121 - 122: 3.469 distance: 121 - 124: 5.927 distance: 122 - 123: 21.998 distance: 122 - 128: 3.950 distance: 124 - 125: 5.283 distance: 124 - 126: 7.670 distance: 125 - 127: 10.532 distance: 128 - 129: 6.540 distance: 129 - 130: 18.182 distance: 129 - 132: 10.068 distance: 130 - 131: 25.676 distance: 130 - 138: 12.392 distance: 132 - 133: 7.794 distance: 133 - 134: 4.329 distance: 133 - 135: 5.436 distance: 134 - 136: 7.136 distance: 135 - 137: 7.672 distance: 136 - 137: 5.144 distance: 138 - 139: 20.977 distance: 139 - 140: 30.842 distance: 139 - 142: 10.375 distance: 140 - 141: 20.132 distance: 140 - 148: 30.551 distance: 142 - 143: 14.099 distance: 143 - 144: 13.368 distance: 143 - 145: 6.016 distance: 144 - 146: 10.900 distance: 145 - 147: 9.253 distance: 146 - 147: 13.958 distance: 148 - 149: 27.494 distance: 149 - 150: 10.188 distance: 149 - 152: 8.589 distance: 150 - 151: 28.646 distance: 150 - 157: 18.854 distance: 152 - 153: 17.987 distance: 153 - 154: 11.619 distance: 154 - 155: 6.706 distance: 155 - 156: 21.788 distance: 157 - 158: 9.994 distance: 157 - 163: 20.885 distance: 158 - 159: 27.200 distance: 158 - 161: 10.447 distance: 159 - 160: 15.771 distance: 159 - 164: 13.938 distance: 161 - 162: 7.315 distance: 162 - 163: 19.062 distance: 164 - 165: 34.815 distance: 165 - 166: 25.353 distance: 166 - 167: 20.046 distance: 166 - 168: 32.903 distance: 168 - 169: 7.360 distance: 169 - 170: 7.698 distance: 170 - 171: 18.904